[Bioc-devel] annotation() to BiocGenerics?

Dear Valerie and other developers,

executing the vignette from package GSVA fails with an error related to the change described in your email (because before it did not appear):

Error: processing vignette ?GSVA.Rnw? failed with diagnostics:
chunk 19
Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function "annotation<-", for signature "ExpressionSet", "missing"
Execution halted

the main function of the package, gsva(), calls at some point 'annotation(eset)' for some ExpressionSet object 'eset'.

i've tried the following solutions:

1. put in NAMESPACE

importFrom(Biobase, annotation)

and replace every call to 'annotation()' by 'Biobase::annotation()'

2. put in NAMESPACE

importFrom(BiocGenerics, annotation)

and replace every call to 'annotation()' by 'BiocGenerics::annotation()'


but none of them work, both give still the same error.

i've executed the vignette interactively and this is the traceback() and sessionInfo() at the line of code producing the error:

gbm_es <- gsva(gbm_eset, brainTxDbSets, mx.diff=FALSE, verbose=FALSE)$es.obs

Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function "annotation<-", for signature "ExpressionSet", "missing"

traceback()

6: stop("unable to find an inherited method for function \"", fdef at generic,
      "\", for signature ", cnames)
5: function (classes, fdef, mtable)
  {
      methods <- .findInheritedMethods(classes, fdef, mtable)
      if (length(methods) == 1L)
          return(methods[[1L]])
      else if (length(methods) == 0L) {
          cnames <- paste0("\"", sapply(classes, as.character),
              "\"", collapse = ", ")
          stop("unable to find an inherited method for function \"",
              fdef at generic, "\", for signature ", cnames)
      }
      else stop("Internal error in finding inherited methods; didn't return a unique method")
  }(list("ExpressionSet", "missing"), function (object, ..., value)
  standardGeneric("annotation<-"), <environment>)
4: Biobase::`annotation<-`(eScoEset, "")
3: .local(expr, gset.idx.list, annotation, ...)
2: gsva(gbm_eset, brainTxDbSets, mx.diff = FALSE, verbose = FALSE)
1: gsva(gbm_eset, brainTxDbSets, mx.diff = FALSE, verbose = FALSE)

whose interpretation goes beyond my expertise, so i hope somebody more experienced than me has a hint about the problem :)

cheers,
robert.

On 09/18/2012 08:48 PM, Valerie Obenchain wrote:

'annotation' and 'annotation<-' have been moved from Biobase (2.17.8) to
BiocGenerics (0.3.2). This should propagate through tomorrows build.

Valerie


On 08/30/2012 11:35 AM, Valerie Obenchain wrote:

Hi Vince,

Yes we can add this to BiocGenerics. I'll post back when it's done.

Valerie


On 08/29/2012 07:25 AM, Vincent Carey wrote:

currently in Biobase

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Robert Castelo, PhD
Associate Professor
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